메뉴 건너뛰기




Volumn 12, Issue 1, 2016, Pages

Evolutionary and Functional Relationships in the Truncated Hemoglobin Family

Author keywords

[No Author keywords available]

Indexed keywords

DISSOCIATION; FORECASTING; HEMOGLOBIN; RATE CONSTANTS;

EID: 84956796262     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004701     Document Type: Article
Times cited : (39)

References (90)
  • 3
    • 77952988108 scopus 로고    scopus 로고
    • A New Generation of Homology Search Tools Based on Probabilistic Inference
    • Eddy S, A New Generation of Homology Search Tools Based on Probabilistic Inference. Genome Inf. 2009;23(1):205–11.
    • (2009) Genome Inf , vol.23 , Issue.1 , pp. 205-211
    • Eddy, S.1
  • 6
    • 10444229578 scopus 로고    scopus 로고
    • Structural Bases for Heme Binding and Diatomic Ligand Recognition in Truncated Hemoglobins
    • Milani M, Pesce A, Nardini M, Ouellet H, Ouellet Y, Dewilde S, et al. Structural Bases for Heme Binding and Diatomic Ligand Recognition in Truncated Hemoglobins. J. Inorg. Biochem. 2005 Jan;99(1):97–109. 15598494
    • (2005) J. Inorg. Biochem , vol.99 , Issue.1 , pp. 97-109
    • Milani, M.1    Pesce, A.2    Nardini, M.3    Ouellet, H.4    Ouellet, Y.5    Dewilde, S.6
  • 8
    • 0035423114 scopus 로고    scopus 로고
    • Mycobacterium tuberculosis Hemoglobin N Displays a Protein Tunnel Suited for O2 Diffusion to the Heme
    • Milani M, Pesce A, Ouellet Y, Ascenzi P, Guertin M, Bolognesi M, Mycobacterium tuberculosis Hemoglobin N Displays a Protein Tunnel Suited for O2 Diffusion to the Heme. EMBO J. 2001 Aug 1;20(15):3902–9. 11483493
    • (2001) EMBO J , vol.20 , Issue.15 , pp. 3902-3909
    • Milani, M.1    Pesce, A.2    Ouellet, Y.3    Ascenzi, P.4    Guertin, M.5    Bolognesi, M.6
  • 10
    • 10644291828 scopus 로고    scopus 로고
    • Nitric Oxide Dioxygenase Function and Mechanism of Flavohemoglobin, Hemoglobin, Myoglobin and their Associated Reductases
    • Gardner P, Nitric Oxide Dioxygenase Function and Mechanism of Flavohemoglobin, Hemoglobin, Myoglobin and their Associated Reductases. J. Inorg. Biochem. 2005;99:247–66. 15598505
    • (2005) J. Inorg. Biochem , vol.99 , pp. 247-266
    • Gardner, P.1
  • 11
    • 84922599930 scopus 로고    scopus 로고
    • Peroxidase Activity and Involvement in the Oxidative Stress Response of Roseobacter denitrificans Truncated Hemoglobin
    • Wang Y, Barbeau X, Bilimoria A, Lagüe P, Couture M, Tang JK-H, Peroxidase Activity and Involvement in the Oxidative Stress Response of Roseobacter denitrificans Truncated Hemoglobin. PLoS One. 2015;10(2).
    • (2015) PLoS One , vol.10 , Issue.2
    • Wang, Y.1    Barbeau, X.2    Bilimoria, A.3    Lagüe, P.4    Couture, M.5    Tang, J.K.-H.6
  • 13
    • 0000610156 scopus 로고
    • Structure of hæemoglobin: A three-dimensional fourier synthesis of reduced human haemoglobin at 5.5 Å resolution
    • Muirhead H, Perutz MF, Structure of hæemoglobin: A three-dimensional fourier synthesis of reduced human haemoglobin at 5.5 Å resolution. Nature. Medical Research Council Laboratory of Molecular Biology, Cambridge; 1963;199(4894):633–8.
    • (1963) Nature. Medical Research Council Laboratory of Molecular Biology, Cambridge , vol.199 , Issue.4894 , pp. 633-638
    • Muirhead, H.1    Perutz, M.F.2
  • 14
    • 0024352104 scopus 로고
    • Heme-dependent Activation of Soluble Guanylate Cyclase by Nitric Oxide: Regulation of Enzyme Activity by Porphyrins and Metalloporphyrins
    • Ignarro L, Heme-dependent Activation of Soluble Guanylate Cyclase by Nitric Oxide: Regulation of Enzyme Activity by Porphyrins and Metalloporphyrins. Semin Hematol. 1989;26(1):63–76. 2564216
    • (1989) Semin Hematol , vol.26 , Issue.1 , pp. 63-76
    • Ignarro, L.1
  • 17
    • 0037059826 scopus 로고    scopus 로고
    • Truncated Hemoglobins: a New Family of Hemoglobins Widely Distributed in Bacteria, Unicellular Eukaryotes, and Plants
    • Wittenberg JB, Bolognesi M, Wittenberg B a, Guertin M, Truncated Hemoglobins: a New Family of Hemoglobins Widely Distributed in Bacteria, Unicellular Eukaryotes, and Plants. J. Biol. Chem. 2002 Jan 11;277(2):871–4. 11696555
    • (2002) J. Biol. Chem , vol.277 , Issue.2 , pp. 871-874
    • Wittenberg, J.B.1    Bolognesi, M.2    Wittenberg, B.3    Guertin, M.4
  • 19
    • 33646341657 scopus 로고    scopus 로고
    • A Phylogenetic and Structural Analysis of Truncated Hemoglobins
    • Vuletich D a, Lecomte JTJ, A Phylogenetic and Structural Analysis of Truncated Hemoglobins. J. Mol. Evol. 2006 Feb;62(2):196–210. 16474979
    • (2006) J. Mol. Evol , vol.62 , Issue.2 , pp. 196-210
    • Vuletich, D.1    Lecomte, J.T.J.2
  • 21
    • 31944445783 scopus 로고    scopus 로고
    • Water and Ligand Entry in Myoglobin: Assessing the Speed and Extent of Heme Pocket Hydration After CO Photodissociation
    • Goldbeck R a, Bhaskaran S, Ortega C, Mendoza JL, Olson JS, Soman J, et al. Water and Ligand Entry in Myoglobin: Assessing the Speed and Extent of Heme Pocket Hydration After CO Photodissociation. Proc. Natl. Acad. Sci. U. S. A. 2006 Jan 31;103(5):1254–9. 16432219
    • (2006) Proc. Natl. Acad. Sci. U. S. A , vol.103 , Issue.5 , pp. 1254-1259
    • Goldbeck, R.1    Bhaskaran, S.2    Ortega, C.3    Mendoza, J.L.4    Olson, J.S.5    Soman, J.6
  • 22
    • 0030773396 scopus 로고    scopus 로고
    • Myoglobin discriminates between O2, NO, and CO by electrostatic interactions with the bound ligand
    • Olson J, Phillips G, Myoglobin discriminates between O2, NO, and CO by electrostatic interactions with the bound ligand. J. Biol. Inorg. Chem. 1997;2:544–52.
    • (1997) J. Biol. Inorg. Chem , vol.2 , pp. 544-552
    • Olson, J.1    Phillips, G.2
  • 23
    • 33746224034 scopus 로고    scopus 로고
    • Ligand interactions in the distal heme pocket of Mycobacterium tuberculosis truncated hemoglobin N: roles of TyrB10 and GlnE11 residues
    • Ouellet Y, Milani M, Couture M, Bolognesi M, Guertin M, Ligand interactions in the distal heme pocket of Mycobacterium tuberculosis truncated hemoglobin N: roles of TyrB10 and GlnE11 residues. Biochemistry. 2006 Jul 25;45(29):8770–81. 16846220
    • (2006) Biochemistry , vol.45 , Issue.29 , pp. 8770-8781
    • Ouellet, Y.1    Milani, M.2    Couture, M.3    Bolognesi, M.4    Guertin, M.5
  • 24
    • 38949211023 scopus 로고    scopus 로고
    • Bond or cage effect: how nitrophorins transport and release nitric oxide
    • Martí M a, González Lebrero MC, Roitberg AE, Estrin D a, Bond or cage effect: how nitrophorins transport and release nitric oxide. J. Am. Chem. Soc. 2008 Feb 6;130(5):1611–8. doi: 10.1021/ja075565a 18189390
    • (2008) J. Am. Chem. Soc , vol.130 , Issue.5 , pp. 1611-1618
    • Martí, M.1    González Lebrero, M.C.2    Roitberg, A.E.3    Estrin, D.4
  • 25
    • 79958242994 scopus 로고    scopus 로고
    • Comparing and Combining Implicit Ligand Sampling with Multiple Steered Molecular Dynamics to Study Ligand Migration Processes in Heme Proteins
    • Forti F, Boechi L, Estrin DA, Marti MA, Comparing and Combining Implicit Ligand Sampling with Multiple Steered Molecular Dynamics to Study Ligand Migration Processes in Heme Proteins. J. Comput. Chem. 2011;32(10):2219–31. doi: 10.1002/jcc.21805 21541958
    • (2011) J. Comput. Chem , vol.32 , Issue.10 , pp. 2219-2231
    • Forti, F.1    Boechi, L.2    Estrin, D.A.3    Marti, M.A.4
  • 26
    • 79955825038 scopus 로고    scopus 로고
    • Role of the Distal Hydrogen-Bonding Network in Regulating Oxygen Affinity in the Truncated Hemoglobin III from Campylobacter jejuni
    • Arroyo Mañez P, Lu C, Boechi L, Martí MA, Shepherd M, Wilson JL, et al. Role of the Distal Hydrogen-Bonding Network in Regulating Oxygen Affinity in the Truncated Hemoglobin III from Campylobacter jejuni. Biochemistry. 2011;50(19):3946–56. doi: 10.1021/bi101137n 21476539
    • (2011) Biochemistry , vol.50 , Issue.19 , pp. 3946-3956
    • Arroyo Mañez, P.1    Lu, C.2    Boechi, L.3    Martí, M.A.4    Shepherd, M.5    Wilson, J.L.6
  • 28
    • 33749179197 scopus 로고    scopus 로고
    • Heme Protein Oxygen Affinity Regulation Exerted by Proximal Effects
    • Capece L, Marti M a, Crespo A, Doctorovich F, Estrin D a, Heme Protein Oxygen Affinity Regulation Exerted by Proximal Effects. J. Am. Chem. Soc. 2006 Sep 27;128(38):12455–61. 16984195
    • (2006) J. Am. Chem. Soc , vol.128 , Issue.38 , pp. 12455-12461
    • Capece, L.1    Marti, M.2    Crespo, A.3    Doctorovich, F.4    Estrin, D.5
  • 30
    • 51849127392 scopus 로고    scopus 로고
    • A Microscopic Study of the Deoxyhemoglobin-Catalyzed Generation of Nitric Oxide from Nitrite Anion
    • Perissinotti LL, Marti MA, Doctorovich F, Luque FJ, Estrin DA, A Microscopic Study of the Deoxyhemoglobin-Catalyzed Generation of Nitric Oxide from Nitrite Anion. Biochemistry. 2008;47(37):9793–802. doi: 10.1021/bi801104c 18717599
    • (2008) Biochemistry , vol.47 , Issue.37 , pp. 9793-9802
    • Perissinotti, L.L.1    Marti, M.A.2    Doctorovich, F.3    Luque, F.J.4    Estrin, D.A.5
  • 31
    • 33845216141 scopus 로고    scopus 로고
    • Time-Resolved Methods in Biophysics. 2. Monitoring Haem Proteins at Work with Nanosecond Laser Flash Photolysis
    • Abbruzzetti S, Bruno S, Faggiano S, Grandi E, Mozzarelli A, Viappiani C, Time-Resolved Methods in Biophysics. 2. Monitoring Haem Proteins at Work with Nanosecond Laser Flash Photolysis. Photochem. Photobiol. Sci. 2006;5(12):1109–20. 17136275
    • (2006) Photochem. Photobiol. Sci , vol.5 , Issue.12 , pp. 1109-1120
    • Abbruzzetti, S.1    Bruno, S.2    Faggiano, S.3    Grandi, E.4    Mozzarelli, A.5    Viappiani, C.6
  • 32
    • 84881096622 scopus 로고    scopus 로고
    • Ligand Migration Through Hemeprotein Cavities: Insights from Laser Flash Photolysis and Molecular Dynamics Simulations
    • Abbruzzetti S, Spyrakis F, Bidon-chanal A, Luque F, Viappiani C, Ligand Migration Through Hemeprotein Cavities: Insights from Laser Flash Photolysis and Molecular Dynamics Simulations. Phys. Chem. Chem. Phys. 2013;15:10686–701. doi: 10.1039/c3cp51149a 23733145
    • (2013) Phys. Chem. Chem. Phys , vol.15 , pp. 10686-10701
    • Abbruzzetti, S.1    Spyrakis, F.2    Bidon-Chanal, A.3    Luque, F.4    Viappiani, C.5
  • 35
    • 55249106911 scopus 로고    scopus 로고
    • Ligand Binding to Truncated Hemoglobin N from Mycobacterium tuberculosis is Strongly Modulated by the Interplay Between the Distal Heme Pocket Residues and Internal Water
    • Ouellet YH, Daigle R, Lagüe P, Dantsker D, Milani M, Bolognesi M, et al. Ligand Binding to Truncated Hemoglobin N from Mycobacterium tuberculosis is Strongly Modulated by the Interplay Between the Distal Heme Pocket Residues and Internal Water. J. Biol. Chem. 2008 Oct 3;283(40):27270–8. doi: 10.1074/jbc.M804215200 18676995
    • (2008) J. Biol. Chem , vol.283 , Issue.40 , pp. 27270-27278
    • Ouellet, Y.H.1    Daigle, R.2    Lagüe, P.3    Dantsker, D.4    Milani, M.5    Bolognesi, M.6
  • 36
    • 84969641396 scopus 로고    scopus 로고
    • Ligand Uptake in Mycobacterium tuberculosis Truncated Hemoglobins is Controlled by Both Internal Tunnels and Active Site Water Molecules
    • Boron I, Bustamante JP, Davidge K, Singh S, Bowman LA, Tinajero-trejo M, et al. Ligand Uptake in Mycobacterium tuberculosis Truncated Hemoglobins is Controlled by Both Internal Tunnels and Active Site Water Molecules. F1000Research. 2015;4(22).
    • (2015) F1000Research , vol.4 , Issue.22
    • Boron, I.1    Bustamante, J.P.2    Davidge, K.3    Singh, S.4    Bowman, L.A.5    Tinajero-Trejo, M.6
  • 37
    • 35348845951 scopus 로고    scopus 로고
    • The Roles of Tyr(CD1) and Trp(G8) in Mycobacterium tuberculosis Truncated Hemoglobin O in Ligand Binding and on the Heme Distal Site Architecture
    • Ouellet H, Milani M, LaBarre M, Bolognesi M, Couture M, Guertin M, The Roles of Tyr(CD1) and Trp(G8) in Mycobacterium tuberculosis Truncated Hemoglobin O in Ligand Binding and on the Heme Distal Site Architecture. Biochemistry. 2007;46:11440–50. 17887774
    • (2007) Biochemistry , vol.46 , pp. 11440-11450
    • Ouellet, H.1    Milani, M.2    LaBarre, M.3    Bolognesi, M.4    Couture, M.5    Guertin, M.6
  • 39
    • 79955783127 scopus 로고    scopus 로고
    • A Hydrogen-Bonding Network Formed by the B10–E7–E11 Residues of a Truncated Hemoglobin from Tetrahymena pyriformis is Critical for Stability of Bound Oxygen and Nitric Oxide Detoxification
    • Igarashi J, Kobayashi K, A Hydrogen-Bonding Network Formed by the B10–E7–E11 Residues of a Truncated Hemoglobin from Tetrahymena pyriformis is Critical for Stability of Bound Oxygen and Nitric Oxide Detoxification. J. Biol. Inorg. Chem. 2011;16:599–609. doi: 10.1007/s00775-011-0761-3 21298303
    • (2011) J. Biol. Inorg. Chem , vol.16 , pp. 599-609
    • Igarashi, J.1    Kobayashi, K.2
  • 40
    • 4043170589 scopus 로고    scopus 로고
    • Thr-E11 Regulates O2 Affinity in Cerebratulus lacteus Mini-hemoglobin
    • Pesce A, Nardini M, Ascenzi P, Geuens E, Dewilde S, Moens L, et al. Thr-E11 Regulates O2 Affinity in Cerebratulus lacteus Mini-hemoglobin. J. Biol. Chem. 2004;279(32):33662–72. 15161908
    • (2004) J. Biol. Chem , vol.279 , Issue.32 , pp. 33662-33672
    • Pesce, A.1    Nardini, M.2    Ascenzi, P.3    Geuens, E.4    Dewilde, S.5    Moens, L.6
  • 41
    • 2542445605 scopus 로고    scopus 로고
    • Tyrosine B10 Inhibits Stabilization of Bound Carbon Monoxide and Oxygen in Soybean Leghemoglobin
    • Kundu S, Blouin G, Premer S, Sarath G, Olson J, Hargrove M, Tyrosine B10 Inhibits Stabilization of Bound Carbon Monoxide and Oxygen in Soybean Leghemoglobin. Biochemistry. 2004;43:6241–52. 15147208
    • (2004) Biochemistry , vol.43 , pp. 6241-6252
    • Kundu, S.1    Blouin, G.2    Premer, S.3    Sarath, G.4    Olson, J.5    Hargrove, M.6
  • 43
    • 0035895937 scopus 로고    scopus 로고
    • Mapping the Pathways for O2 Entry Into and Exit from Myoglobin
    • Scott EE, Gibson QH, Olson JS, Mapping the Pathways for O2 Entry Into and Exit from Myoglobin. J. Biol. Chem. 2001;276:5177–88. 11018046
    • (2001) J. Biol. Chem , vol.276 , pp. 5177-5188
    • Scott, E.E.1    Gibson, Q.H.2    Olson, J.S.3
  • 44
    • 84861326102 scopus 로고    scopus 로고
    • Myoglobin and Mitochondria: A Relationship Bound by Oxygen and Nitric Oxide
    • Kamga C, Krishnamurthy S, Shiva S, Myoglobin and Mitochondria: A Relationship Bound by Oxygen and Nitric Oxide. Nitric Oxide. 2012;26(4):251–8. doi: 10.1016/j.niox.2012.03.005 22465476
    • (2012) Nitric Oxide , vol.26 , Issue.4 , pp. 251-258
    • Kamga, C.1    Krishnamurthy, S.2    Shiva, S.3
  • 45
    • 34249819653 scopus 로고    scopus 로고
    • Dynamical Regulation of Ligand Migration by a Gate-Opening Molecular Switch in Truncated Hemoglobin-N from Mycobacterium tuberculosis
    • Bidon-Chanal A, Marti MA, Estrin DA, Luque FJ, Dynamical Regulation of Ligand Migration by a Gate-Opening Molecular Switch in Truncated Hemoglobin-N from Mycobacterium tuberculosis. J. Am. Chem. Soc. 2007;129:6782–8. 17488073
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 6782-6788
    • Bidon-Chanal, A.1    Marti, M.A.2    Estrin, D.A.3    Luque, F.J.4
  • 46
    • 33745593982 scopus 로고    scopus 로고
    • Ligand-Induced Dynamical Regulation of NO Conversion in Mycobacterium tuberculosis Truncated Hemoglobin-N
    • Bidon-chanal A, Martı MA, Crespo A, Milani M, Orozco M, Bolognesi M, et al. Ligand-Induced Dynamical Regulation of NO Conversion in Mycobacterium tuberculosis Truncated Hemoglobin-N. Proteins. 2007;464(May 2006):457–64.
    • (2007) Proteins , vol.464 , pp. 457-464
    • Bidon-Chanal, A.1    Martı, M.A.2    Crespo, A.3    Milani, M.4    Orozco, M.5    Bolognesi, M.6
  • 47
    • 16244367739 scopus 로고    scopus 로고
    • Theoretical Study of the Truncated Hemoglobin HbN: Exploring the Molecular Basis of the NO Detoxification Mechanism
    • Crespo A, Martí MA, Kalko SG, Morreale A, Orozco M, Gelpi JL, et al. Theoretical Study of the Truncated Hemoglobin HbN: Exploring the Molecular Basis of the NO Detoxification Mechanism. J. Am. Chem. Soc. 2005 Mar 30;127(12):4433–44. 15783226
    • (2005) J. Am. Chem. Soc , vol.127 , Issue.12 , pp. 4433-4444
    • Crespo, A.1    Martí, M.A.2    Kalko, S.G.3    Morreale, A.4    Orozco, M.5    Gelpi, J.L.6
  • 48
    • 67649831231 scopus 로고    scopus 로고
    • Role of pre-A Motif in Nitric Oxide Scavenging by Truncated Hemoglobin, HbN, of Mycobacterium tuberculosis
    • Lama A, Pawaria S, Bidon-Chanal A, Anand A, Gelpi JL, Arya S, et al. Role of pre-A Motif in Nitric Oxide Scavenging by Truncated Hemoglobin, HbN, of Mycobacterium tuberculosis. J. Biol. Chem. 2009;284(21):14457–68. doi: 10.1074/jbc.M807436200 19329431
    • (2009) J. Biol. Chem , vol.284 , Issue.21 , pp. 14457-14468
    • Lama, A.1    Pawaria, S.2    Bidon-Chanal, A.3    Anand, A.4    Gelpi, J.L.5    Arya, S.6
  • 49
  • 50
    • 34147154024 scopus 로고    scopus 로고
    • Reaction of Mycobacterium tuberculosis Truncated Hemoglobin O with Hydrogen Peroxide: Evidence for Peroxidatic Activity and Formation of Protein-based Radicals
    • Ouellet H, Ranguelova K, Labarre M, Wittenberg JB, Wittenberg BA, Magliozzo RS, et al. Reaction of Mycobacterium tuberculosis Truncated Hemoglobin O with Hydrogen Peroxide: Evidence for Peroxidatic Activity and Formation of Protein-based Radicals. J. Biol. Chem. 2007;282(10):7491–503. 17218317
    • (2007) J. Biol. Chem , vol.282 , Issue.10 , pp. 7491-7503
    • Ouellet, H.1    Ranguelova, K.2    Labarre, M.3    Wittenberg, J.B.4    Wittenberg, B.A.5    Magliozzo, R.S.6
  • 51
    • 72049095862 scopus 로고    scopus 로고
    • Peroxidase-Like Activity of Thermobifida fusca Hemoglobin: The Oxidation of Dibenzylbutanolide
    • Torge R, Comandini A, Catacchio B, Bonamore A, Botta B, Boffi A, Peroxidase-Like Activity of Thermobifida fusca Hemoglobin: The Oxidation of Dibenzylbutanolide. J. Mol. Catal. B Enzym. 2009 Dec;61(3–4):303–8.
    • (2009) J. Mol. Catal. B Enzym , vol.61 , Issue.3-4 , pp. 303-308
    • Torge, R.1    Comandini, A.2    Catacchio, B.3    Bonamore, A.4    Botta, B.5    Boffi, A.6
  • 54
    • 0017411710 scopus 로고
    • The Protein Data Bank: a Computer-Based Archival File for Macromolecular Structures
    • Bernstein F, Koetzle T, Williams G, Meyer E, Brice M, Rodgers J, et al. The Protein Data Bank: a Computer-Based Archival File for Macromolecular Structures. J. Mol. Biol. 1977;112(3):535–42. 875032
    • (1977) J. Mol. Biol , vol.112 , Issue.3 , pp. 535-542
    • Bernstein, F.1    Koetzle, T.2    Williams, G.3    Meyer, E.4    Brice, M.5    Rodgers, J.6
  • 55
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated Profile HMM Searches
    • Eddy S, Accelerated Profile HMM Searches. PLoS Comput. Biol. 2011;7(10).
    • (2011) PLoS Comput. Biol , vol.7 , Issue.10
    • Eddy, S.1
  • 56
    • 77949601825 scopus 로고    scopus 로고
    • CD-HIT Suite: a Web Server for Clustering and Comparing Biological Sequences
    • Huang Y, Niu B, Gao Y, Fu L, Li W, CD-HIT Suite: a Web Server for Clustering and Comparing Biological Sequences. Bioinformatics. 2010;26(5):680–2. doi: 10.1093/bioinformatics/btq003 20053844
    • (2010) Bioinformatics , vol.26 , Issue.5 , pp. 680-682
    • Huang, Y.1    Niu, B.2    Gao, Y.3    Fu, L.4    Li, W.5
  • 58
    • 65449188232 scopus 로고    scopus 로고
    • Jalview Version 2—a multiple sequence alignment editor and analysis workbench
    • Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ, Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009;25(9):1189–91. doi: 10.1093/bioinformatics/btp033 19151095
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1189-1191
    • Waterhouse, A.M.1    Procter, J.B.2    Martin, D.M.A.3    Clamp, M.4    Barton, G.J.5
  • 59
    • 77954403053 scopus 로고    scopus 로고
    • BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
    • Criscuolo A, Gribaldo S, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 2010 Jan;10:210. doi: 10.1186/1471-2148-10-210 20626897
    • (2010) BMC Evol. Biol , vol.10 , pp. 210
    • Criscuolo, A.1    Gribaldo, S.2
  • 61
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: Selection of Best-fit Models of Protein Evolution
    • Abascal F, Zardoya R, Posada D, ProtTest: Selection of Best-fit Models of Protein Evolution. Bioinformatics. 2005;21(9):2104–5. 15647292
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 62
    • 79960004119 scopus 로고    scopus 로고
    • Interactive Tree Of Life v2: Online Annotation and Display of Phylogenetic Trees made Easy
    • Letunic I, Bork P, Interactive Tree Of Life v2: Online Annotation and Display of Phylogenetic Trees made Easy. Nucleic Acids Res. 2011;
    • (2011) Nucleic Acids Res
    • Letunic, I.1    Bork, P.2
  • 63
    • 77954554764 scopus 로고    scopus 로고
    • An Automated Stochastic Approach to the Identification of the Protein Specificity Determinants and Functional Subfamilies
    • Mazin P, Gelfand M, Mironov A, Rakhmaninova A, Rubinov A, Russell R, et al. An Automated Stochastic Approach to the Identification of the Protein Specificity Determinants and Functional Subfamilies. Algorithms Mol. Biol. 2010;5(29).
    • (2010) Algorithms Mol. Biol , vol.5 , Issue.29
    • Mazin, P.1    Gelfand, M.2    Mironov, A.3    Rakhmaninova, A.4    Rubinov, A.5    Russell, R.6
  • 67
    • 84938211607 scopus 로고    scopus 로고
    • Structural Flexibility of the Heme Cavity in the Cold-Adapted Truncated Hemoglobin from the Antarctic Marine Bacterium Pseudoalteromas haloplanktis TAC125
    • Giordano D, Pesce A, Boechi L, Bustamante JP, Caldelli E, Howes BD, et al. Structural Flexibility of the Heme Cavity in the Cold-Adapted Truncated Hemoglobin from the Antarctic Marine Bacterium Pseudoalteromas haloplanktis TAC125. Fed. Eur. Biochem. Soc. J. 2015;282(15):2948–65.
    • (2015) Fed. Eur. Biochem. Soc. J , vol.282 , Issue.15 , pp. 2948-2965
    • Giordano, D.1    Pesce, A.2    Boechi, L.3    Bustamante, J.P.4    Caldelli, E.5    Howes, B.D.6
  • 69
    • 0001398008 scopus 로고    scopus 로고
    • How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules?
    • Wang J, Cieplak P, Kollman PA, How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules? J. Comput. Chem. 2000;21(12):1049–74.
    • (2000) J. Comput. Chem , vol.21 , Issue.12 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 71
    • 83455262978 scopus 로고    scopus 로고
    • Molecular Basis for the Substrate Stereoselectivity in Tryptophan Dioxygenase
    • Capece L, Lewis-ballester A, Marti MA, Estrin DA, Yeh S, Molecular Basis for the Substrate Stereoselectivity in Tryptophan Dioxygenase. Biochemistry. 2011;50:10910–8. doi: 10.1021/bi201439m 22082147
    • (2011) Biochemistry , vol.50 , pp. 10910-10918
    • Capece, L.1    Lewis-Ballester, A.2    Marti, M.A.3    Estrin, D.A.4    Yeh, S.5
  • 72
    • 81555214663 scopus 로고    scopus 로고
    • Ligand Migration in Methanosarcina acetivorans Protoglobin: Effects of Ligand Binding and Dimeric Assembly
    • Forti F, Boechi L, Bikiel D, Martí MA, Nardini M, Bolognesi M, et al. Ligand Migration in Methanosarcina acetivorans Protoglobin: Effects of Ligand Binding and Dimeric Assembly. J. Phys. Chem. B. 2011;115(46):13771–80. doi: 10.1021/jp208562b 21985496
    • (2011) J. Phys. Chem. B , vol.115 , Issue.46 , pp. 13771-13780
    • Forti, F.1    Boechi, L.2    Bikiel, D.3    Martí, M.A.4    Nardini, M.5    Bolognesi, M.6
  • 73
    • 63049114012 scopus 로고    scopus 로고
    • The Hemoglobins of the Sub-Antarctic Fish Cottoperca gobio, a Phyletically Basal Species—Oxygen-Binding Equilibria, Kinetics and Molecular Dynamics
    • Giordano D, Boechi L, Samuni U, Vergara A, Martı MA, Estrin A, et al. The Hemoglobins of the Sub-Antarctic Fish Cottoperca gobio, a Phyletically Basal Species—Oxygen-Binding Equilibria, Kinetics and Molecular Dynamics. FEBS J. 2009;276:2266–77. doi: 10.1111/j.1742-4658.2009.06954.x 19292863
    • (2009) FEBS J , vol.276 , pp. 2266-2277
    • Giordano, D.1    Boechi, L.2    Samuni, U.3    Vergara, A.4    Martı, M.A.5    Estrin, A.6
  • 74
    • 84555177994 scopus 로고    scopus 로고
    • Fluoride as a Probe for H-bonding Interactions in the Active Site of Heme Proteins: the Case of Thermobifida fusca Hemoglobin
    • Nicoletti FP, Droghetti E, Boechi L, Bonamore A, Sciamanna N, Estrin D a, et al. Fluoride as a Probe for H-bonding Interactions in the Active Site of Heme Proteins: the Case of Thermobifida fusca Hemoglobin. J. Am. Chem. Soc. 2011 Dec 28;133(51):20970–80. doi: 10.1021/ja209312k 22091531
    • (2011) J. Am. Chem. Soc , vol.133 , Issue.51 , pp. 20970-20980
    • Nicoletti, F.P.1    Droghetti, E.2    Boechi, L.3    Bonamore, A.4    Sciamanna, N.5    Estrin, D.6
  • 75
    • 84920094601 scopus 로고    scopus 로고
    • Interplay of the H-bond Donor-Acceptor Role of the Distal Residues in the Hydroxyl Ligand Stabilization of Thermobifida fusca Truncated Hemoglobin
    • Nicoletti FP, Bustamante JP, Droghetti E, Howes BD, Fittipaldi M, Bonamore A, et al. Interplay of the H-bond Donor-Acceptor Role of the Distal Residues in the Hydroxyl Ligand Stabilization of Thermobifida fusca Truncated Hemoglobin. Biochemistry. 2014;53(51):8021–30. doi: 10.1021/bi501132a 25437272
    • (2014) Biochemistry , vol.53 , Issue.51 , pp. 8021-8030
    • Nicoletti, F.P.1    Bustamante, J.P.2    Droghetti, E.3    Howes, B.D.4    Fittipaldi, M.5    Bonamore, A.6
  • 76
    • 0029633186 scopus 로고
    • AMBER, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules
    • Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, IIIDeBolt S, et al. AMBER, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules. Comput. Phys. Commun. 1995;91(1–3):1–41.
    • (1995) Comput. Phys. Commun , vol.91 , Issue.1-3 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham, T.E.5    DeBolt, S.6
  • 77
    • 47049083320 scopus 로고    scopus 로고
    • Finding Gas Migration Pathways in Proteins using Implicit Ligand Sampling
    • Cohen J, Olsen KW, Schulten K, Finding Gas Migration Pathways in Proteins using Implicit Ligand Sampling. Methods Enzymol. 2008 Jan;437(07):439–57.
    • (2008) Methods Enzymol , vol.437 , Issue.7 , pp. 439-457
    • Cohen, J.1    Olsen, K.W.2    Schulten, K.3
  • 78
    • 84863638846 scopus 로고    scopus 로고
    • Following Ligand Migration Pathways from Picoseconds to Milliseconds in Type II Truncated Hemoglobin from Thermobifida fusca
    • Marcelli A, Abbruzzetti S, Bustamante JP, Feis A, Bonamore A, Boffi A, et al. Following Ligand Migration Pathways from Picoseconds to Milliseconds in Type II Truncated Hemoglobin from Thermobifida fusca. PLoS One. 2012 Jan;7(7):e39884. doi: 10.1371/journal.pone.0039884 22792194
    • (2012) PLoS One , vol.7 , Issue.7 , pp. 39884
    • Marcelli, A.1    Abbruzzetti, S.2    Bustamante, J.P.3    Feis, A.4    Bonamore, A.5    Boffi, A.6
  • 79
    • 0346885688 scopus 로고    scopus 로고
    • A DFT-based QM-MM Approach Designed for the Treatment of large Molecular Systems: Application to Chorismate Mutase
    • Crespo A, Scherlis DA, Martí MA, Ordejón P, Roitberg AE, Estrin DA, A DFT-based QM-MM Approach Designed for the Treatment of large Molecular Systems: Application to Chorismate Mutase. J. Phys. Chem. B. 2003;107(49):13728–36.
    • (2003) J. Phys. Chem. B , vol.107 , Issue.49 , pp. 13728-13736
    • Crespo, A.1    Scherlis, D.A.2    Martí, M.A.3    Ordejón, P.4    Roitberg, A.E.5    Estrin, D.A.6
  • 80
    • 4243943295 scopus 로고    scopus 로고
    • Generalized gradient approximation made simple
    • Perdew JP, Burke K, Ernzerhof M, Generalized gradient approximation made simple. Phys. Rev. Lett. 1996;77(18):3865–8. 10062328
    • (1996) Phys. Rev. Lett , vol.77 , Issue.18 , pp. 3865-3868
    • Perdew, J.P.1    Burke, K.2    Ernzerhof, M.3
  • 81
    • 0037168603 scopus 로고    scopus 로고
    • Spin-Dependent Mechanism for Diatomic Ligand Binding to Heme
    • Franzen S, Spin-Dependent Mechanism for Diatomic Ligand Binding to Heme. Proc. Natl. Acad. Sci. U. S. A. 2002;99(26):16754–9. 12477933
    • (2002) Proc. Natl. Acad. Sci. U. S. A , vol.99 , Issue.26 , pp. 16754-16759
    • Franzen, S.1
  • 82
    • 1942533441 scopus 로고    scopus 로고
    • The Crystal Structure of Synechocystis Hemoglobin with a Covalent Heme Linkage
    • Hoy J, Kundu S, Trent J, IIIRamaswamy S, Hargrove M, The Crystal Structure of Synechocystis Hemoglobin with a Covalent Heme Linkage. J. Biol. Chem. 2004;276(16):16535–42.
    • (2004) J. Biol. Chem , vol.276 , Issue.16 , pp. 16535-16542
    • Hoy, J.1    Kundu, S.2    Trent, J.3    Ramaswamy, S.4    Hargrove, M.5
  • 83
    • 33845674111 scopus 로고    scopus 로고
    • Influence of the Protein Matrix on Intramolecular Histidine Ligatin in Ferric and Ferrous Hexacoordinate Hemoglobins
    • Halder P, Trent III J, Hargrove M, Influence of the Protein Matrix on Intramolecular Histidine Ligatin in Ferric and Ferrous Hexacoordinate Hemoglobins. Proteins Struct. Funct. Bioformatics. 2007;66:172–82.
    • (2007) Proteins Struct. Funct. Bioformatics , vol.66 , pp. 172-182
    • Halder, P.1    Trent III, J.2    Hargrove, M.3
  • 84
    • 0033866598 scopus 로고    scopus 로고
    • Structural Investigations of the Hemoglobin of the Cyanobacterium Synechocystis PCC6803 Reveal a Unique Distal Heme Pocket
    • Couture M, Das T, Savard P-Y, Ouellet Y, Wittenberg J, Wittenberg B, et al. Structural Investigations of the Hemoglobin of the Cyanobacterium Synechocystis PCC6803 Reveal a Unique Distal Heme Pocket. Eur. J. Biochem. 2000;267:4770–80. 10903511
    • (2000) Eur. J. Biochem , vol.267 , pp. 4770-4780
    • Couture, M.1    Das, T.2    Savard, P.-Y.3    Ouellet, Y.4    Wittenberg, J.5    Wittenberg, B.6
  • 85
    • 0037018935 scopus 로고    scopus 로고
    • Truncated hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002: evidence for hexacoordination and covalent adduct formation in the ferric recombinant protein
    • Scott E, Falzone C, Vuletich D, Zhao J, Bryant D, Lecomte J, Truncated hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002: evidence for hexacoordination and covalent adduct formation in the ferric recombinant protein. Biochemistry. 2002;41(22):6902–10. 12033922
    • (2002) Biochemistry , vol.41 , Issue.22 , pp. 6902-6910
    • Scott, E.1    Falzone, C.2    Vuletich, D.3    Zhao, J.4    Bryant, D.5    Lecomte, J.6
  • 87
    • 84904610521 scopus 로고    scopus 로고
    • Characterization of THB1, a Chlamydomonas reinhardtii truncated hemoglobin: linkage to nitrogen metabolism and identification of lysine as the distal heme ligand
    • Johnson E, Rice S, Preimesberger M, Nye D, Gilevicius L, Wenke B, et al. Characterization of THB1, a Chlamydomonas reinhardtii truncated hemoglobin: linkage to nitrogen metabolism and identification of lysine as the distal heme ligand. Biochemistry. 2014;53(28):4573–89. doi: 10.1021/bi5005206 24964018
    • (2014) Biochemistry , vol.53 , Issue.28 , pp. 4573-4589
    • Johnson, E.1    Rice, S.2    Preimesberger, M.3    Nye, D.4    Gilevicius, L.5    Wenke, B.6
  • 88
    • 0000653346 scopus 로고    scopus 로고
    • A Dissociative Mechanism for Reactions of Nitric Oxide with Water Soluble Iron(III) Porphyrins
    • Laverman L, Hoshino M, Ford P, A Dissociative Mechanism for Reactions of Nitric Oxide with Water Soluble Iron(III) Porphyrins. J. Am. Chem. Soc. 1997;119:12663–4.
    • (1997) J. Am. Chem. Soc , vol.119 , pp. 12663-12664
    • Laverman, L.1    Hoshino, M.2    Ford, P.3
  • 89
    • 0035965748 scopus 로고    scopus 로고
    • Mechanistic Studies of Nitric Oxide Reactions with Water Soluble Iron(II), Cobalt(II), and Iron(III) Porphyrin Complexes in Aqueous Solutions: Implications for Biological Activity
    • Laverman L, Ford P, Mechanistic Studies of Nitric Oxide Reactions with Water Soluble Iron(II), Cobalt(II), and Iron(III) Porphyrin Complexes in Aqueous Solutions: Implications for Biological Activity. J. Am. Chem. Soc. 2001;123:11614–22. 11716716
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 11614-11622
    • Laverman, L.1    Ford, P.2
  • 90
    • 34547372841 scopus 로고    scopus 로고
    • Simulation of Heme Using DFT + U: A Step toward Accurate Spin-State Energetics
    • Scherlis D, Cococcioni M, Sit P, Marzari N, Simulation of Heme Using DFT + U: A Step toward Accurate Spin-State Energetics. J. Phys. Chem. B. 2007;111:7384–91. 17547444
    • (2007) J. Phys. Chem. B , vol.111 , pp. 7384-7391
    • Scherlis, D.1    Cococcioni, M.2    Sit, P.3    Marzari, N.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.